The phenomenon of fluxionality in the reactions of transition metal oxide clusters provides many opportunities in various catalytic and industrial processes. To gain a better understanding into the various factors influencing this phenomenon, we have carried out an electronic structure investigation of the fluxionality pathways when W3O6- and Mo3O6- clusters react with hydrogen sulfide and ammonia. The study illustrates how the metal (W vs Mo), different spin states of the anionic metal oxide cluster (doublet vs quartet), and the nature of the nonmetal in the small molecule (0 vs S vs N), all affect the fluxionality pathway. The thermodynamically facile fluxionality pathway with H2S detaches both the hydrogens from hydrogen sulfide and can thus be very useful in the petrochemical and desulfurization industries. The fluxionality pathway with NH3 results in interesting metal-bound imines and bridged amines. However, the overall fluxionality process with NH3 is found to be thermodynamically unfavorable.